diff --git a/doc/changes/devel/13280.bugfix.rst b/doc/changes/devel/13280.bugfix.rst
new file mode 100644
index 00000000000..6d03da603f2
--- /dev/null
+++ b/doc/changes/devel/13280.bugfix.rst
@@ -0,0 +1 @@
+Fixed bug where :func:`mne.preprocessing.maxwell_filter_prepare_emptyroom` would not reliably identify meg channel types for matching bads across emptyroom and task, by `Harrison Ritz`_.
diff --git a/mne/preprocessing/maxwell.py b/mne/preprocessing/maxwell.py
index 47c5b52e0c6..7d247ab137d 100644
--- a/mne/preprocessing/maxwell.py
+++ b/mne/preprocessing/maxwell.py
@@ -167,7 +167,12 @@ def maxwell_filter_prepare_emptyroom(
     elif bads == "keep":
         bads = raw_er_prepared.info["bads"]
 
-    bads = [ch_name for ch_name in bads if ch_name.startswith("MEG")]
+    # Filter to only include MEG channels
+    meg_ch_names = [
+        raw_er_prepared.ch_names[pick]
+        for pick in pick_types(raw_er_prepared.info, meg=True, exclude=[])
+    ]
+    bads = [ch_name for ch_name in bads if ch_name in meg_ch_names]
     raw_er_prepared.info["bads"] = bads
 
     # handle dev_head_t